Eh, the hardlines are bolted to the bottom of the plenum. Most people take them off, but it's really just aesthetics at that point if they did the bypass correctly, and I think you would notice if it was incorrectly done.
I am leaning to turbos as well with those compression numbers however. I think Medallion suggestion regarding taking your intake/intercooler plumbing apart to check for oil is a good one at this point.